LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -46.182620 0.0000000) to (32.656044 46.182620 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0755430 5.9070793 4.9800000 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -46.182620 0.0000000) to (32.656044 46.182620 4.9800000) create_atoms CPU = 0.002 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0755430 5.9070793 4.9800000 Created 696 atoms using lattice units in orthogonal box = (0.0000000 -46.182620 0.0000000) to (32.656044 46.182620 4.9800000) create_atoms CPU = 0.002 seconds 696 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1376 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_500937681860_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5674.4314 0 -5674.4314 78059.147 59 0 -6099.8774 0 -6099.8774 8300.3886 Loop time of 7.84979 on 1 procs for 59 steps with 1376 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5674.43138760098 -6099.8733609298 -6099.87737028456 Force two-norm initial, final = 532.36737 0.21784526 Force max component initial, final = 82.974861 0.022273314 Final line search alpha, max atom move = 1.0000000 0.022273314 Iterations, force evaluations = 59 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.8174 | 7.8174 | 7.8174 | 0.0 | 99.59 Neigh | 0.010106 | 0.010106 | 0.010106 | 0.0 | 0.13 Comm | 0.011396 | 0.011396 | 0.011396 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01086 | | | 0.14 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254.00 ave 6254 max 6254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122416.0 ave 122416 max 122416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122416 Ave neighs/atom = 88.965116 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -6099.8774 0 -6099.8774 8300.3886 15021.091 64 0 -6100.1385 0 -6100.1385 -42.41043 15087.963 Loop time of 0.57089 on 1 procs for 5 steps with 1376 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6099.87737028455 -6100.13839575799 -6100.1384859247 Force two-norm initial, final = 149.42982 1.0558610 Force max component initial, final = 129.86446 0.90847435 Final line search alpha, max atom move = 0.00047340440 0.00043007575 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56789 | 0.56789 | 0.56789 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048725 | 0.00048725 | 0.00048725 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00251 | | | 0.44 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6275.00 ave 6275 max 6275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121584.0 ave 121584 max 121584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121584 Ave neighs/atom = 88.360465 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.204 | 5.204 | 5.204 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6100.1385 0 -6100.1385 -42.41043 Loop time of 2.805e-06 on 1 procs for 0 steps with 1376 atoms 142.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.805e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6261.00 ave 6261 max 6261 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121296.0 ave 121296 max 121296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121296 Ave neighs/atom = 88.151163 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.204 | 5.204 | 5.204 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -6100.1385 -6100.1385 32.661859 92.713279 4.9825054 -42.41043 -42.41043 12.958689 -43.671417 -96.518561 2.3542237 936.9851 Loop time of 2.399e-06 on 1 procs for 0 steps with 1376 atoms 250.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.399e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6261.00 ave 6261 max 6261 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60648.0 ave 60648 max 60648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121296.0 ave 121296 max 121296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121296 Ave neighs/atom = 88.151163 Neighbor list builds = 0 Dangerous builds = 0 1376 -6100.1384859247 eV 2.35422370147026 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08